tbuckley/cabot-search huggingface dataset:
Possibilities of Ultrasound Diagnostics of Post-Radiation Lung Damage: Initial Experience
Authors: Yu. V. Kabin, M. Yu. Shivilova, S. L. Shvyrev, V. V. Kapustin
Journal: Radiology - Practice (2023)

The article deals with the ultrasound diagnostics of the post radiation lung damage in 44 patients aged 32–73 years who received radiation therapy in the form of distance radiation therapy (DRT) for breast cancer. In all patients total focal dose (TFD) of radiation was 50 Gy with classical fractionation. The main types of subpleural post radiation injury, their intensity and prevalence were determined. The ultrasound findings were compared with CT images of patients six months after the start of DRT.
Diagnostic Capabilities of Cone-Beam Computed Tomography in the Detection of Pathological Conditions of the Craniovertebral Region. Part 1 – analysis
Authors: A. D. Gukova, Ya. A. Lubashev
Journal: Radiology - Practice (2023)

For the timely detection of pathology, as well as in order to avoid overdiagnosis, it is important to create criteria for diagnosing the pathology of the craniovertebral zone in adults and children, taking into account their anatomical and physiological features. To date, the questions of the optimal method of radiodiagnosis of patients with pathology of the craniovertebral region are insufficiently voluminous and clearly defined. Despite the advantages, cone beam computed tomography is still not widely used in everyday clinical diagnostic practice for the study of the craniovertebral region in the population. The use of the technique of cone beam computed tomography could greatly facilitate radiological diagnosis for the detection of anomalies and pathological conditions of the craniovertebral region.
Comparative Characteristics of High-Resolution Ultrasonic and Magnetic Resonance Imaging in the Diagnostics of Edema after Plastic Facial Contouring (Clinical Case)
Authors: A. Yu. Vasil’ev, D. A. Lezhnev, I. N. Bondarenko, S. A. Magomedova
Journal: Radiology - Practice (2023)

Clinical monitoring of the parameters of high-resolution ultrasound and magnetic resonance imaging (MRI) in the diagnosis of edema after injection contour plastic. When fillers were detected, hypoechoic avascular structures were found in the soft tissues of the face with blurred contours against the background of infiltrative changes. On MRI the filler was more clearly visualized in the fat suppression mode as a signal section with clear, even contours of certain shapes subcutaneously and supraperiostal. Infiltration changes were characterized by signal amplification and contour blurring.
Aspects of Choosing the Technique of Computed Tomography in the Diagnostics of Maxillofacial Dysostosis
Authors: N. I. Imshenetskaya, D. A. Lezhnev, O. Z. Topol’nitskiy, V. V. Petrovskaya
Journal: Radiology - Practice (2023)

Maxillofacial dysostoses are congenital malformations of organs of head and neck, developing from the I and II gill arches. It is important to carry out differential diagnostics based on a comprehensive basic and additional examination aimed at determining all intracranial and extracranial symptoms specific for concrete syndrome, which is possible with modern methods of radiological diagnostic — CBCT and MSCT. The purpose of the study is to determine key aspects of choosing the computed tomography technique for diagnostics of maxillofacial dysostoses. From 2009 to 2023 215 MSCT and 86 CBCT were performed in 211 patients aged from 2 to 18 years old with maxillofacial dysostoses for the purpose of differential diagnostics of pathology, indications for choosing the volume of radiological examination were determined.
Assessment of the Status of Resection Margins in Patients with Breast Cancer During Breast-Conserving Surgery Using Intraoperative Mammography
Authors: Ya. I. Bondarchuk, S. S. Bagnenko, A. V. Chernaya, P. V. Krivorot’ko, A. S. Artemyeva, E. K. Zhiltsova, N. Amirov
Journal: Radiology - Practice (2023)

The results of surgical treatment of 56 patients were analyzed. All patients were undergone on breast-conserving surgery with intraoperative X-ray control on a mammographic digital device. The mean time to complete the study was 10 minutes, which did not significantly affect the duration of the operation. Of the 56 studied preparations after breast-conserving surgery, a positive resection margin (R1) was found in 1 case during a planned histological examination, which is associated with a high X-ray density of the patient’s breast tissue. In 2 cases, positive resection margins (DCIS) were detected, additional excision made it possible to avoid repeated surgical intervention. In 1 case, a false positive result was obtained, which did not negatively affect the results of surgical treatment. There were no false negative results.
The Effect of Glycemic Status on the X-ray Image of Pulmonary Tuberculosis in Patients with Type 2 Diabetes Mellitus
Authors: Yu. A. Chaadaeva, N. A. Gorbunov, A. P. Dergilev, Ya. L. Manakova, V. I. Kochura
Journal: Radiology - Practice (2023)

The study is devoted to determining the effect of the level of glycemic status, on the X-ray picture in patients with type 2 diabetes mellitus. The X-ray archive of 82 patients with pulmonary tuberculosis and type 2 diabetes mellitus was analyzed. The evaluation of the radiological picture was carried out with the correlation of the level of glucose in the blood. In patients with fasting glucose values of 10 mmol/l and above, the X-ray picture of tuberculosis was characterized by extensive areas of lung tissue consolidation, with a 50 % frequency of localization in the lower sections, with the rapid formation of decay cavities. The course of tuberculosis with severe tuberculous intoxication was observed in patients with sharp jumps in the daily blood glucose index of more than 5 mmol/l, even in patients with an average glucose index of no more than 8 mmol/l. The X-ray picture was characterized by the presence of areas of consolidation in the lungs on both sides with many air cavities and dropout foci; the appearance of new areas of consolidation against the background of anti-tuberculosis therapy.
Effects of COVID-19 on cognition and brain health
Authors: Sijia Zhao, Sofia Toniolo, Adam Hampshire, Masud Husain
Journal: Trends in Cognitive Sciences (2023)

COVID-19 is associated with a range of neurological, cognitive, and mental health symptoms both acutely and chronically that can persist for many months after infection in people with long-COVID syndrome. Investigations of cognitive function and neuroimaging have begun to elucidate the nature of some of these symptoms. They reveal that, although cognitive deficits may be related to brain imaging abnormalities in some people, symptoms can also occur in the absence of objective cognitive deficits or neuroimaging changes. Furthermore, cognitive impairment may be detected even in asymptomatic individuals. We consider the evidence regarding symptoms, cognitive deficits, and neuroimaging, as well as their possible underlying mechanisms.
Health-related Quality of Life Profile of Newly Diagnosed Patients With Myelodysplastic Syndromes by Age, Sex, and Risk Group: A Real-world Study by the GIMEMA
Authors: Fabio Efficace, Wael Al Essa, Uwe Platzbecker, Pasquale Niscola, Giuseppe A. Palumbo, Giovanni Caocci, Francesco Cottone, Massimo Breccia, Mario Luppi, Reinhard Stauder, Alessandra Ricco, Duska Petranovic, Frederic Baron, Maria Teresa Voso, Luana Fianchi, Chiara Frairia, Isabella Capodanno, Chiara Sarlo, Marilena Fedele, Roberto Massimo Lemoli, Rosangela Invernizzi, Daniele Vallisa, Nicola Di Renzo, Claudio Fozza, Maribel Doro, Johannes M. Giesinger, Marco Vignetti
Journal: HemaSphere (2023)

Health-related quality of life (HRQoL) is an important goal of therapy for patients with myelodysplastic syndromes (MDS); however, little is known about HRQoL of these patients at clinical presentation. We report HRQoL profile of newly diagnosed patients with MDS across both the the International Prognostic Scoring System (IPSS) and IPSS-Revised (IPSS-R) classifications, stratified by sex and age group categories, aiming to also establish European Organization for Research and Treatment of Cancer Quality of Life Questionnaire-Core30 (EORTC QLQ-C30) reference values for these patients. Analysis was based on 927 patients with a median age of 73.3 years (interquartile range, 66.0-79.2), of whom 506 and 421 with lower- and higher-risk disease respectively, according to the IPSS classification. HRQoL was assessed with the EORTC QLQ-C30 and substantial differences by age groups and sex, between and within lower- and higher-risk disease categories were observed. For example, within higher-risk disease patients, the youngest group (ie, 30-59 years) tended to report clinically meaningful worse outcomes across various functional and symptom domains compared with older age groups. We also developed 2 regression models allowing for the prediction of EORTC QLQ-C30 reference scores for patients classified according to either the IPSS or the IPSS-R. Investigation of prevalence rates for clinically important problems and symptoms at diagnosis revealed a substantial burden of the disease with >50% of patients reporting clinically important problems with physical functioning and dyspnea in both lower- and higher-risk disease. Our findings may help to enhance the interpretation of HRQoL outcomes in future MDS studies and to better contextualize HRQoL data from routine practice settings.
Linking serum vitamin D levels with gut microbiota after 1-year lifestyle intervention with Mediterranean diet in patients with obesity and metabolic syndrome: a nested cross-sectional and prospective study
Authors: Hatim Boughanem, Patricia Ruiz-Limón, Jesús Pilo, José Manuel Lisbona-Montañez, Francisco J. Tinahones, Isabel Moreno Indias, Manuel Macías-González
Journal: Gut Microbes (2023)

Vitamin D, microbiota, and the Mediterranean diet (MedDiet) have been the focus of recent research due to their potential role in maintaining overall health. We hypothesize that MedDiet may alter the gut microbiota profile through changes in vitamin D levels. We aimed to investigate changes in gut microbiota and serum vitamin D levels after a MedDiet within a lifestyle intervention. The study included 91 patients with obesity and metabolic syndrome, who were categorized based on their serum vitamin D levels as having either optimal or low 25-hydroxyvitamin D [25(OH)D levels]. The profile of the gut microbiota was analyzed by the 16S rRNA sequencing, inferring its functionality through PICRUsT. Participants underwent a hypocaloric MedDiet and change in their lifestyle for 1 year, and the profile and functionality of their gut microbiota were evaluated by analyzing inter-individual differences in time. At baseline, gut microbiota profiles qualitatively differed between participants with Optimal or Low 25(OH)D levels [Unweighted (p = 0.016)]. Moreover, participants with Optimal 25(OH)D levels showed a higher gut microbiota diversity than those with Low 25(OH)D levels (p < 0.05). The differential analysis of abundance between the Low and Optimal 25(OH)D groups revealed differences in the levels of Bacteroides, Prevotella, and two Clostridiales features. After 1-year dietary intervention, both groups increased their 25(OH)D levels. Furthermore, both groups did not show significant differences in gut microbiota diversity, although the Low 25(OH)D group showed greater improvement in gut microbiota diversity by comparing at baseline and after dietary intervention (p < 0.05). Changes in specific bacterial taxa were observed within each group but did not differ significantly between the groups. Metabolic pathway analysis indicated differences in microbial functions between the groups (p < 0.05). These findings suggest that 25(OH)D status is associated with gut microbiota composition, diversity, and functionality, and lifestyle intervention can modulate both gut microbiota and 25(OH)D levels, potentially influencing metabolic pathways.
A DNA adenine demethylase impairs PRC2-mediated repression of genes marked by a specific chromatin signature
Authors: Qingxiao Jia, Xinran Zhang, Qian Liu, Junjie Li, Wentao Wang, Xuan Ma, Bo Zhu, Sheng Li, Shicheng Gong, Jingjing Tian, Meng Yuan, Yu Zhao, Dao-Xiu Zhou
Journal: Genome biology (2023)

Abstract Background The Fe (II)- and α-ketoglutarate-dependent AlkB family dioxygenases are implicated in nucleotide demethylation. AlkB homolog1 (ALKBH1) is shown to demethylate DNA adenine methylation (6mA) preferentially from single-stranded or unpaired DNA, while its demethylase activity and function in the chromatin context are unclear. Results Here, we find that loss-of-function of the rice ALKBH1 gene leads to increased 6mA in the R-loop regions of the genome but has a limited effect on the overall 6mA level. However, in the context of mixed tissues, rather than on individual loci, the ALKBH1 mutation or overexpression mainly affects the expression of genes with a specific combination of chromatin modifications in the body region marked with H3K4me3 and H3K27me3 but depleted of DNA CG methylation. In the similar context of mixed tissues, further analysis reveals that the ALKBH1 protein preferentially binds to genes marked by the chromatin signature and has a function to maintain a high H3K4me3/H3K27me3 ratio by impairing the binding of Polycomb repressive complex 2 (PRC2) to the targets, which is required for both the basal and stress-induced expression of the genes. Conclusion Our findings unravel a function of ALKBH1 to control the balance between the antagonistic histone methylations for gene activity and provide insight into the regulatory mechanism of PRC2-mediated H3K27me3 deposition within the gene body region.
Beyond the anti-PD-1/PD-L1 era: promising role of the BTLA/HVEM axis as a future target for cancer immunotherapy
Authors: Christian Sordo-Bahamonde, Seila Lorenzo-Herrero, Rocío Granda-Díaz, Alejandra Martínez-Pérez, Candelaria Aguilar-García, Juan P. Rodrigo, Juana M. García-Pedrero, Segundo Gonzalez
Journal: Molecular Cancer (2023)

Recent introduction of monoclonal antibodies targeting immune checkpoints to harness antitumor immunity has revolutionized the cancer treatment landscape. The therapeutic success of immune checkpoint blockade (ICB)-based therapies mainly relies on PD-1/PD-L1 and CTLA-4 blockade. However, the limited overall responses and lack of reliable predictive biomarkers of patient´s response are major pitfalls limiting immunotherapy success. Hence, this reflects the compelling need of unveiling novel targets for immunotherapy that allow to expand the spectrum of ICB-based strategies to achieve optimal therapeutic efficacy and benefit for cancer patients. This review thoroughly dissects current molecular and functional knowledge of BTLA/HVEM axis and the future perspectives to become a target for cancer immunotherapy. BTLA/HVEM dysregulation is commonly found and linked to poor prognosis in solid and hematological malignancies. Moreover, circulating BTLA has been revealed as a blood-based predictive biomarker of immunotherapy response in various cancers. On this basis, BTLA/HVEM axis emerges as a novel promising target for cancer immunotherapy. This prompted rapid development and clinical testing of the anti-BTLA blocking antibody Tifcemalimab/icatolimab as the first BTLA-targeted therapy in various ongoing phase I clinical trials with encouraging results on preliminary efficacy and safety profile as monotherapy and combined with other anti-PD-1/PD-L1 therapies. Nevertheless, it is anticipated that the intricate signaling network constituted by BTLA/HVEM/CD160/LIGHT involved in immune response regulation, tumor development and tumor microenvironment could limit therapeutic success. Therefore, in-depth functional characterization in different cancer settings is highly recommended for adequate design and implementation of BTLA-targeted therapies to guarantee the best clinical outcomes to benefit cancer patients.
BNIP3 as a potential biomarker for the identification of prognosis and diagnosis in solid tumours
Authors: Qin Yu, Wenhao Fu, Yutang Fu, Wenjing Ye, Huiqiong Yan, Zecheng Yu, Ruirui Li, Yili Cai, Yuxin Chen, Lingyun Wang, Xianqiao Wei, Yangkun Chen, Yuheng Zhang, Huazhong Ying, Furong Tang, Fangwei Dai, Wei Han
Journal: Molecular Cancer (2023)

Abstract Background Traditional radiotherapy and chemotherapy have been intensively studied for their role in the treatment of tumours. However, these therapies often cause side effects for patients, which calls for the development of novel treatment options for tumours. B-cell lymphoma-2 (Bcl-2)/adenovirus E1B 19 kDa-interacting protein 3 (BNIP3) reportedly apoptosis-inducing effects in tumour cells and is associated with the progression and treatment of multiple tumours. Nevertheless, little is known about its potential role in tumour diagnosis and targeted therapy. Findings The results of the study demonstrated that the interaction of BNIP3 with HDAC1 may affect the progression of breast invasive cancer (BRCA), sarcoma (SARC), kidney renal clear cell carcinoma (KIRC), and low-grade glioma (LGG). BNIP3 seemed to exert its effects in BRCA and SARC primarily through gene silencing and integrator complex, and in KIRC and LGG, mainly by affecting olfactory function, suggesting that targeted therapy can be developed based on the above signalling pathway and downstream molecules. Interpretation BNIP3 has emerged as a promising therapeutic and diagnostic target for BRCA, SARC, KIRC, and LGG, providing new insights into tumour molecular therapies in the clinic.
The screening, identification, design and clinical application of tumor-specific neoantigens for TCR-T cells
Authors: Jiangping Li, Zhiwen Xiao, Donghui Wang, Lei Jia, Shihong Nie, Xingda Zeng, Wei Hu
Journal: Molecular Cancer (2023)

Recent advances in neoantigen research have accelerated the development of tumor immunotherapies, including adoptive cell therapies (ACTs), cancer vaccines and antibody-based therapies, particularly for solid tumors. With the development of next-generation sequencing and bioinformatics technology, the rapid identification and prediction of tumor-specific antigens (TSAs) has become possible. Compared with tumor-associated antigens (TAAs), highly immunogenic TSAs provide new targets for personalized tumor immunotherapy and can be used as prospective indicators for predicting tumor patient survival, prognosis, and immune checkpoint blockade response. Here, the identification and characterization of neoantigens and the clinical application of neoantigen-based TCR-T immunotherapy strategies are summarized, and the current status, inherent challenges, and clinical translational potential of these strategies are discussed.
Chaperone‐mediated autophagy: Molecular mechanisms, biological functions, and diseases
Authors: Ruchen Yao, Jun Shen
Journal: MedComm (2023)

Chaperone-mediated autophagy (CMA) is a lysosomal degradation pathway that eliminates substrate proteins through heat-shock cognate protein 70 recognition and lysosome-associated membrane protein type 2A-assisted translocation. It is distinct from macroautophagy and microautophagy. In recent years, the regulatory mechanisms of CMA have been gradually enriched, including the newly discovered NRF2 and p38-TFEB signaling, as positive and negative regulatory pathways of CMA, respectively. Normal CMA activity is involved in the regulation of metabolism, aging, immunity, cell cycle, and other physiological processes, while CMA dysfunction may be involved in the occurrence of neurodegenerative disorders, tumors, intestinal disorders, atherosclerosis, and so on, which provides potential targets for the treatment and prediction of related diseases. This article describes the general process of CMA and its role in physiological activities and summarizes the connection between CMA and macroautophagy. In addition, human diseases that concern the dysfunction or protective role of CMA are discussed. Our review deepens the understanding of the mechanisms and physiological functions of CMA and provides a summary of past CMA research and a vision of future directions.
Correction: Are haematopoietic stem cell transplants stem cell transplants, is there a threshold dose of CD34-positive cells and how many are needed for rapid posttransplant granulocyte recovery?
Authors: Junren Chen, Robert Peter Gale, Yahui Feng, Yu Hu, Saibing Qi, Xueou Liu, Huaiping Zhu, Xiaowen Gong, Wei Zhang, Huilan Liu, Zimin Sun
Journal: Leukemia (2023)
Thymol targeting interleukin 4 induced 1 expression reshapes the immune microenvironment to sensitize the immunotherapy in lung adenocarcinoma
Authors: Tong Li, Jie Shi, Longlong Wang, Xuan Qin, Rui Zhou, Ming Dong, Fan Ren, Xin Li, Zihe Zhang, Yanan Chen, Yanhua Liu, Yongjun Piao, Yi Shi, Song Xu, Jun Chen, Jia Li
Journal: MedComm (2023)

Immune checkpoint blockades are the most promising therapy in lung adenocarcinoma (LUAD). However, the response rate remains limited, underscoring the urgent need for effective sensitizers. Interleukin 4 induced 1 (IL4I1) is reported to have immunoinhibitory and tumor-promoting effects in several cancers. However, the targetable value of IL4I1 in sensitizing the immunotherapy is not clear, and there is a lack of effective small molecules that specifically target IL4I1. Here, we show that silencing IL4I1 significantly remodels the immune microenvironment via inhibiting aryl hydrocarbon receptor (AHR) signaling, thereby enhancing the efficacy of anti-PD-1 antibody in LUAD, which suggests that IL4I1 is a potential drug target for the combination immunotherapy. We then identify thymol as the first small molecule targeting IL4I1 transcription through a drug screening. Thymol inhibits the IL4I1 expression and blocks AHR signaling in LUAD cells. Thymol treatment restores the antitumor immune response and suppresses the progression of LUAD in an orthotopic mouse model. Strikingly, the combination treatment of thymol with anti-PD-1 antibody shows significant tumor regression in LUAD mice. Thus, we demonstrate that thymol is an effective small molecule to sensitize the PD-1 blockade in LUAD via targeting IL4I1, which provides a novel strategy for the immunotherapy of LUAD.
Frequent ZNF217 mutations lead to transcriptional deregulation of interferon signal transduction via altered chromatin accessibility in B cell lymphoma
Authors: Franziska Briest, Daniel Noerenberg, Cornelius Hennch, Kenichi Yoshida, Raphael Hablesreiter, Jose Nimo, Daniel Sasca, Marieluise Kirchner, Larry Mansouri, Yoshikage Inoue, Laura Wiegand, Annette M. Staiger, Beatrice Casadei, Penelope Korkolopoulou, January Weiner, Armando Lopez-Guillermo, Arne Warth, Tamás Schneider, Ákos Nagy, Wolfram Klapper, Michael Hummel, George Kanellis, Ioannis Anagnostopoulos, Philipp Mertins, Lars Bullinger, Richard Rosenquist, Theodoros P. Vassilakopoulos, German Ott, Seishi Ogawa, Frederik Damm
Journal: Leukemia (2023)

Abstract Recent exome-wide studies discovered frequent somatic mutations in the epigenetic modifier ZNF217 in primary mediastinal B cell lymphoma (PMBCL) and related disorders. As functional consequences of ZNF217 alterations remain unknown, we comprehensively evaluated their impact in PMBCL. Targeted sequencing identified genetic lesions affecting ZNF217 in 33% of 157 PMBCL patients. Subsequent gene expression profiling ( n = 120) revealed changes in cytokine and interferon signal transduction in ZNF217 -aberrant PMBCL cases. In vitro, knockout of ZNF217 led to changes in chromatin accessibility interfering with binding motifs for crucial lymphoma-associated transcription factors. This led to disturbed expression of interferon-responsive and inflammation-associated genes, altered cell behavior, and aberrant differentiation. Mass spectrometry demonstrates that ZNF217 acts within a histone modifier complex containing LSD1, CoREST and HDAC and interferes with H3K4 methylation and H3K27 acetylation. Concluding, our data suggest non-catalytic activity of ZNF217, which directs histone modifier complex function and controls B cell differentiation-associated patterns of chromatin structure.